Bottom Line:
With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist?We ask you, please, to read the instructions carefully.The time has come: you may turn over your papers...

Affiliation: School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK. teresa.k.attwood@manchester.ac.uk

ABSTRACTWe live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...

Figure 4: Example output from the ChemSpider Journal of ChemistryMarked-up chemical entities include chemical families, chemical names (pale orange highlights), chemical groups (dark green) and reaction types, with links out to Wikipedia where appropriate (e.g. overlaid here as a ‘callout’). Displayed mark-up is controlled via the Article Mark-up toolbar, shown on the right-hand side of the screen-shot. (http://www.chemmantis.com). The extract from The ChemSpider Journal of Chemistry ([49]; Walker, M.A. (2009) Some highlights in synthetic organic methodology, article 895), has been reproduced by permission of The Royal Society of Chemistry.

Mentions:
The ChemSpider Journal of Chemistry is another experiment set up to demonstrate the added value that Web technologies can offer in terms of enriching published information. The Journal spans a range of chemistry-related subjects, including chemical biology, chemo-informatics and molecular modelling. Its articles are marked up using the Chemistry Markup And Nomenclature Transformation Integrated System, ChemMantis. ChemMantis identifies and extracts chemical names, converting them into chemical structures using name-to-structure conversion algorithms and dictionary look-ups in the ChemSpider chemistry database (which provides access to almost 21.5 million unique chemical entities); it also marks up a range of other chemical entities, including chemical families, groups, elements and reaction types; where appropriate, the terms are linked to their Wikipedia definitions (see Figure 4). A facility is also provided to allow readers to comment on individual articles.

Figure 4: Example output from the ChemSpider Journal of ChemistryMarked-up chemical entities include chemical families, chemical names (pale orange highlights), chemical groups (dark green) and reaction types, with links out to Wikipedia where appropriate (e.g. overlaid here as a ‘callout’). Displayed mark-up is controlled via the Article Mark-up toolbar, shown on the right-hand side of the screen-shot. (http://www.chemmantis.com). The extract from The ChemSpider Journal of Chemistry ([49]; Walker, M.A. (2009) Some highlights in synthetic organic methodology, article 895), has been reproduced by permission of The Royal Society of Chemistry.

Mentions:
The ChemSpider Journal of Chemistry is another experiment set up to demonstrate the added value that Web technologies can offer in terms of enriching published information. The Journal spans a range of chemistry-related subjects, including chemical biology, chemo-informatics and molecular modelling. Its articles are marked up using the Chemistry Markup And Nomenclature Transformation Integrated System, ChemMantis. ChemMantis identifies and extracts chemical names, converting them into chemical structures using name-to-structure conversion algorithms and dictionary look-ups in the ChemSpider chemistry database (which provides access to almost 21.5 million unique chemical entities); it also marks up a range of other chemical entities, including chemical families, groups, elements and reaction types; where appropriate, the terms are linked to their Wikipedia definitions (see Figure 4). A facility is also provided to allow readers to comment on individual articles.

Bottom Line:
With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist?We ask you, please, to read the instructions carefully.The time has come: you may turn over your papers...

Affiliation:
School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK. teresa.k.attwood@manchester.ac.uk

ABSTRACTWe live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...